Antimicrobial Resistance:Do we know everything?Dr. Sid ThakurAssistant ProfessorSwine Health & ProductionCVM, NCSU
Research FocusAntimicrobial ResistancePathogen detection, Phenotypic &Genotypic CharacterizationOnfarm, Slaughter, Retail,...
Antimicrobial Resistance:Lost in Translation !!!Are bacterial pathogens smarter than humans ?
Pathogen Evolution:How good bacteria go bad Difference between good and bad pathogen Few genes encoded on plasmids or ch...
EID Global Trends1940-2004 EID are dominated by zoonoses (60.3 %)Jones et al.,Nature, 2008DrugResistantZoonoticWildlife
 NDM-1 (New Delhi metallo- β- Lactamase) Escherichia coli and Klebsiella pneumoniae Dec 2009 in India; Pakistan, US, UK...
Antimicrobials: Farm to TableSanitizers DisinfectantsFood Tissue TreatmentsAquacultureAnimalAgricultureHumansPlantAgricult...
Back to susceptible population:Is it so simple?AntimicrobialResistantAntimicrobialSusceptibleAntimicrobialExposureTreatmen...
Reservoirs of AntimicrobialResistance determinants Focus is on the commodity Food animals, produce, humans Role of Envi...
Soil Antibiotic ResistosomeVanessa et al.,Science, 2006
Bacteria subsisting on antibioticsDantas et al., Science, 2008
Role of trucks inPathogen dissemination All in all out swine production system Four truck wash systems were selected tha...
Role of Truck Washin Pathogen Dissemination0102030405060708090100%PositiveTruck Wash A Truck Wash B Truck Wash C Truck Was...
Plasmid exchange inSalmonella positive pigsS. Typhimurium S. MuenchenCh. Pl Ch. Pl1 2 3 4- 23 kb- 9.4 kb-6.5 kb-4.3 kb-2.3...
DANMAP Data-2011DANMAP, 2011
S. Typhimurium AntimicrobialResistance profile: PigsDANMAP, 2011
S. Typhimurium AR:Pigs, pork and human casesDANMAP, 2011
Campylobacter jejuni:Antimicrobial ResistanceDANMAP, 2011
FQ consumption: HumansDANMAP, 2011
DANMAP 2011 Report:Key HighlightsDANMAP, 2011
NARMS Retail meat (Poultry)Antimicrobial Resistance DataC. jejuniCIP/NAL
Are resistant pathogens arebetter fit to survive in vivo ?Luo, et al., PNAS, 2005 No Fluoroquinolone (FQ) selection press...
Antibiotic Exposed Antibiotic-free (ABF) Use of antimicrobials Intensive Indoor No use of antimicrobials Extensive O...
Sampling SchemeConventional Farm ( All-in -All-out)10 cohorts (35 pigs/cohort)Farrowing Nursery FinishingTruckTruck8 days ...
Antimicrobial Free Systemwater, feed, swabs,soil (n=5 each)LariageTruck (n=5 each)Environment at Farm and Slaughterwater, ...
AntimicrobialsAZI CIP ERY GEN TET FFN NAL TEL CLI MDRResistance%020406080100ABFConventionalPig v/s EnvironmentAntimicrobia...
Key OutcomesCampylobacter and C. difficilePigEnvironmentAntimicrobialExposedAntimicrobialfree (ABF)AntimicrobialResistantS...
C. coli Population TreeABF pigs and carcassABF env at farm and slg.Conv pigs and carcassConv env at farm and slg.ST-5776ST...
PhylogeneticsClustering of STsConventional systemABF systemProd. System Unique STsABF 14Conventional 32ST-5764ST-5770, ST-...
Clostridium difficile AR ProfileAntimicrobialsTET AMP MET ERY CIP VAN MDRResistance%020406080100ABFCONVENTIONALFarmAntimic...
Salmonella Serotypes A total of 1090 Salmonella isolates 24 different Salmonella serotypes
Salmonella CampylobacterA; AmpicillinC: ChloramphenicolS: StreptomycinSu: SulfamethoxazoleT: TetracyclineS. TyphimuriumAR ...
Salmonella Genotypic SimilarityPFGE pattern Antimicrobials Serotype Farm StageSample typeA-Antimicrobial Free System; C- C...
LagoonSprayer/effluent5 plotsDay 0, BeforeApplication• 10 Lagoon• 5 Effluent• 25* SoilDay 0, AfterApplication• 25 Soilsamp...
020406080100Before D0 D7 D14 Before D0 D7 D14SalmonellaPrevalence%Farm1 Farm2Preliminary Results
Summary• Move away from a generalized discussion onantimicrobial resistance solution• Pathogen ecological niche: specifice...
Questions(www.tmelab.org)
Dr. Sid Thakur - Antimicrobial Resistance: Do We Know Everything?
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Dr. Sid Thakur - Antimicrobial Resistance: Do We Know Everything?

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Antimicrobial Resistance: Do We Know Everything? - Dr. Sid Thakur, Assistant Professor, North Carolina State University, from the 2013 NIAA Merging Values and Technology conference, April 15-17, 2013, Louisville, KY, USA.

More presentations at http://www.trufflemedia.com/agmedia/conference/2013-niaa-merging-values-and-technology

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  • Slow down here…Stress on drug resistance on ABF pigs
  • Post chill positivebecos due to slaughter house effect there is no blast chilling system
  • Dr. Sid Thakur - Antimicrobial Resistance: Do We Know Everything?

    1. 1. Antimicrobial Resistance:Do we know everything?Dr. Sid ThakurAssistant ProfessorSwine Health & ProductionCVM, NCSU
    2. 2. Research FocusAntimicrobial ResistancePathogen detection, Phenotypic &Genotypic CharacterizationOnfarm, Slaughter, Retail, HumanSample & EnvironmentMolecular Characterization:Mechanisms of resistance Transfer of resistance Virulence genesDevelop Sensitive and RapidDetection Tests Microarray Real-time PCRGlobal Epidemiology
    3. 3. Antimicrobial Resistance:Lost in Translation !!!Are bacterial pathogens smarter than humans ?
    4. 4. Pathogen Evolution:How good bacteria go bad Difference between good and bad pathogen Few genes encoded on plasmids or chromosome E. coli (commensal) : E. coli O157: H7 (HUS)Stephens & Murray, Current Biology, 2001 Raskin et al., Cell, 2006
    5. 5. EID Global Trends1940-2004 EID are dominated by zoonoses (60.3 %)Jones et al.,Nature, 2008DrugResistantZoonoticWildlife
    6. 6.  NDM-1 (New Delhi metallo- β- Lactamase) Escherichia coli and Klebsiella pneumoniae Dec 2009 in India; Pakistan, US, UK, Japan, Brazil International TravelEmergence of a new ARmechanism in IndiaNumber of cases by CountrySweden (Dec 2009): 1st reportIndia (March 2010): 1st reportUSA (June 2010): 3 casesIndia (June 2010): More casesUK (Aug 2010): 37 casesCanada (Aug 2010): 1st reportJapan (Sept 2010): 1 reportAll the patients had a travel history toIndia within the past one year
    7. 7. Antimicrobials: Farm to TableSanitizers DisinfectantsFood Tissue TreatmentsAquacultureAnimalAgricultureHumansPlantAgriculture FoodretailFoodServiceFoodProcessingHomeAntibioticsBiocides Food GradePreservativesAntimicrobial soaps/lotionsPersonal hygieneproductsFood Tissue TreatmentsSanitizers DisinfectantsFood Tissue TreatmentsSanitizers DisinfectantsSanitizers DisinfectantsFungicides
    8. 8. Back to susceptible population:Is it so simple?AntimicrobialResistantAntimicrobialSusceptibleAntimicrobialExposureTreatmentEnvironmentTreatmentTreatmentAntimicrobialResistantAntimicrobialResistant
    9. 9. Reservoirs of AntimicrobialResistance determinants Focus is on the commodity Food animals, produce, humans Role of Environment• Limited research conducted• Need to focus more on the environment• Study environmental reservoirs• Food animals: Farm environment (lagoon, truck, lairage)• Produce: Water for irrigation, birds, manure• Humans: Hospital environment, community
    10. 10. Soil Antibiotic ResistosomeVanessa et al.,Science, 2006
    11. 11. Bacteria subsisting on antibioticsDantas et al., Science, 2008
    12. 12. Role of trucks inPathogen dissemination All in all out swine production system Four truck wash systems were selected thatservice one integrated system.– Samples obtained from each wash station• 10 trucks pre-wash, 5 swabs from each• 10 trucks post-wash, 5 swabs from each Fecal samples were also collected on farm, atslaughter (Cecal content & MLN) & lairageApplied Environmental Microbiology, 2009Breeding/Farrowing Nursery Finishing
    13. 13. Role of Truck Washin Pathogen Dissemination0102030405060708090100%PositiveTruck Wash A Truck Wash B Truck Wash C Truck Wash DTruck Wash Salmonella Prevalence - Pre and Post WashPre WashPost WashA = recycled water and Virkon-S B = recycled water and phenolC = fresh water, soap, and phenol D = recycled water and phenol0102030405060708090100%PositiveTruck Wash A Truck Wash B Truck Wash C Truck Wash DTruck Wash Campylobacter Prevalence - Pre and Post WashPre WashPost Wash Salmonella and Campylobacter isolatesat farm were different from those isolatedat the slaughter plant (Cecal content and MLN) Isolates from the Cecum and MLN weresimilar to those isolated from the truck floor
    14. 14. Plasmid exchange inSalmonella positive pigsS. Typhimurium S. MuenchenCh. Pl Ch. Pl1 2 3 4- 23 kb- 9.4 kb-6.5 kb-4.3 kb-2.3 kb-2.0 kbConjugation AnalysisSouthern HybridizationaphA1-Iab probeAKSSuT ACKSSuTGebreyes and Thakur, AEM, 2005
    15. 15. DANMAP Data-2011DANMAP, 2011
    16. 16. S. Typhimurium AntimicrobialResistance profile: PigsDANMAP, 2011
    17. 17. S. Typhimurium AR:Pigs, pork and human casesDANMAP, 2011
    18. 18. Campylobacter jejuni:Antimicrobial ResistanceDANMAP, 2011
    19. 19. FQ consumption: HumansDANMAP, 2011
    20. 20. DANMAP 2011 Report:Key HighlightsDANMAP, 2011
    21. 21. NARMS Retail meat (Poultry)Antimicrobial Resistance DataC. jejuniCIP/NAL
    22. 22. Are resistant pathogens arebetter fit to survive in vivo ?Luo, et al., PNAS, 2005 No Fluoroquinolone (FQ) selection pressure in this modelFQ sensitiveC. jejuniFQ resistantC. jejuniFQ sensitiveand FQ resistantC. jejuniFQ sensitiveC. jejuniFQ resistantC. jejuniFQ resistantC. jejuni
    23. 23. Antibiotic Exposed Antibiotic-free (ABF) Use of antimicrobials Intensive Indoor No use of antimicrobials Extensive OutdoorUSDA-NIFA StudySalmonella, Campylobacter & ClostridiumVS
    24. 24. Sampling SchemeConventional Farm ( All-in -All-out)10 cohorts (35 pigs/cohort)Farrowing Nursery FinishingTruckTruck8 days old 6,10 weeks 16,26 weeksLairageSlaughterTruck Kill FloorPre-Evis ChillingPost-EvisMLN, Carcass Swab Carcass SwabEnvironment samples ( n=5 each) at farmFeed Water Swab Lagoon Soil TruckEnvironment samples ( n=5 each) at SlaughterLairage Truck
    25. 25. Antimicrobial Free Systemwater, feed, swabs,soil (n=5 each)LariageTruck (n=5 each)Environment at Farm and Slaughterwater, feed, swabs,soil (n=5 each)water, feed, swabs,soil (n=5 each)Farrowing—Nursery--FinishingRotate onnew landSlaughterTruck• Post evis• MLN• Post chill8 cohorts35 pigs/cohort
    26. 26. AntimicrobialsAZI CIP ERY GEN TET FFN NAL TEL CLI MDRResistance%020406080100ABFConventionalPig v/s EnvironmentAntimicrobialsAZI CIP ERY GEN TET FFN NAL TEL CLI MDRResistance%020406080100ABFConventionalEnvironmentSwineAZI = azithromycin, ERY = erythromycin, CIP = ciprofloxacin , GEN = gentamicin, TET =tetracycline, FFN = florfenicol, NAL = nalidixic acid, TEL = telithromycin, CLI = clindamycin;Macarena and Thakur, Applied Environmental Microbiology, 2012
    27. 27. Key OutcomesCampylobacter and C. difficilePigEnvironmentAntimicrobialExposedAntimicrobialfree (ABF)AntimicrobialResistantStrainsAntimicrobialResistantStrains
    28. 28. C. coli Population TreeABF pigs and carcassABF env at farm and slg.Conv pigs and carcassConv env at farm and slg.ST-5776ST-854ST-1068ST-1186
    29. 29. PhylogeneticsClustering of STsConventional systemABF systemProd. System Unique STsABF 14Conventional 32ST-5764ST-5770, ST-1827, ST-1109, ST-5772ST-5248Macarena and Thakur, PLOS ONE, 2012
    30. 30. Clostridium difficile AR ProfileAntimicrobialsTET AMP MET ERY CIP VAN MDRResistance%020406080100ABFCONVENTIONALFarmAntimicrobialsTET AMP MET ERY CIP VAN MDRResistance%020406080100ABFCONVENTIONALEnvironmentAMP: Ampicillin; CIP: Ciprofloxacin; ERY: Erythromycin; MET: Metronidazole;TET: Tetracycline; VAN: Vancomycin; MDR: Multidrug ResistanceSusick and Thakur, Veterinary Microbiology, 2012
    31. 31. Salmonella Serotypes A total of 1090 Salmonella isolates 24 different Salmonella serotypes
    32. 32. Salmonella CampylobacterA; AmpicillinC: ChloramphenicolS: StreptomycinSu: SulfamethoxazoleT: TetracyclineS. TyphimuriumAR Pattern: ACSSuTS. TyphimuriumAR Pattern: SSuTSlaughterCarcassEcological NicheFarmFarm
    33. 33. Salmonella Genotypic SimilarityPFGE pattern Antimicrobials Serotype Farm StageSample typeA-Antimicrobial Free System; C- Conventional System
    34. 34. LagoonSprayer/effluent5 plotsDay 0, BeforeApplication• 10 Lagoon• 5 Effluent• 25* SoilDay 0, AfterApplication• 25 SoilsamplesDay 7• 25 SoilsamplesDay 14• 25 Soilsamples*5 replicates for the five 1m2 plots, 20m apartSalmonella environmentaltransmission from swine manureSAMPLE COLLECTION
    35. 35. 020406080100Before D0 D7 D14 Before D0 D7 D14SalmonellaPrevalence%Farm1 Farm2Preliminary Results
    36. 36. Summary• Move away from a generalized discussion onantimicrobial resistance solution• Pathogen ecological niche: specificenvironment• Renew focus on the role of environment• Antimicrobial resistance is a global problem
    37. 37. Questions(www.tmelab.org)

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